GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Sphingomonas koreensis DSMZ 15582

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate Ga0059261_2771 Ga0059261_2771 3-hydroxybutyrate dehydrogenase

Query= uniprot:B2T9V3
         (247 letters)



>FitnessBrowser__Korea:Ga0059261_2771
          Length = 261

 Score =  140 bits (353), Expect = 3e-38
 Identities = 92/258 (35%), Positives = 137/258 (53%), Gaps = 17/258 (6%)

Query: 5   LAGKTALITAAGQGIGLATAELFAREGARVIATDIR-----------IDGLAGKPVEARK 53
           L+GK+A++T +  GIGLA A+  A EGA V+                ++ L+G       
Sbjct: 3   LSGKSAIVTGSTSGIGLAIAKALAAEGASVMINGFGDAAAIETERAGLEALSGGKALYDG 62

Query: 54  LDVRDDAAIKALA----AEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRM 109
            D+    AI A+     AE+G  D++ N AG  H   I +   E WD    +N+ + + M
Sbjct: 63  ADMSKPDAIYAMVERCHAELGGPDIIVNNAGIQHVAAIEDFPPEKWDAIIAINLSSAWHM 122

Query: 110 IRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRC 169
           +RA +P M     G IIN +SA S V   PN+ AY A+K  + GLTK++A +  T GV  
Sbjct: 123 MRAAVPHMKAAKWGRIINTASAHSLVAS-PNKSAYVAAKHGIAGLTKTIALETATDGVTV 181

Query: 170 NAICPGTVASPSLEQRIVAQAQAQGATLDAV-QAAFVARQPMGRIGKPEEIAALALYLGS 228
           N I PG V +P +E +I    +A+  T + V     +A QP  +  +PE+IAAL ++L  
Sbjct: 182 NCISPGYVWTPLVENQIPDTMKARNMTREQVMNDVLLAAQPTKQFVQPEQIAALLVFLCR 241

Query: 229 DESSFTTGHAHVIDGGWS 246
           DE+S  TG  + +DGGW+
Sbjct: 242 DEASAITGANYTMDGGWT 259


Lambda     K      H
   0.320    0.133    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 155
Number of extensions: 12
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 247
Length of database: 261
Length adjustment: 24
Effective length of query: 223
Effective length of database: 237
Effective search space:    52851
Effective search space used:    52851
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory